Analysis of MCF10A in 16 different conditions 2 biological replicates per sample
| x | |
|---|---|
| GM_none_1 | 1.0413622 |
| GM_none_2 | 1.0386257 |
| IM_none_1 | 0.8367807 |
| IM_none_2 | 1.0293793 |
| IM_none_Glut_1 | 0.9100924 |
| IM_none_Glut_2 | 1.0176144 |
| IM_none_EGF_1 | 0.6407299 |
| IM_none_EGF_2 | 1.0277762 |
| IM_none_noIns_1 | 0.9469116 |
| IM_none_noIns_2 | 1.0188349 |
| IM_none_noGluc_1 | 1.0644846 |
| IM_none_noGluc_2 | 0.8601419 |
| IM_none_noHC_1 | 1.1798928 |
| IM_none_noHC_2 | 1.0055447 |
| IM_none_noCT_1 | 1.0370370 |
| IM_none_noCT_2 | 1.0229394 |
| IM_none_AMPKact_1 | 1.0236837 |
| IM_none_AMPKact_2 | 1.0987349 |
| IM_none_AKTinhib_1 | 1.0697025 |
| IM_none_AKTinhib_2 | 1.1299165 |
| IM_none_ERKinhib_1 | 1.0214759 |
| IM_none_ERKinhib_2 | 1.1492214 |
| IM_none_mTORC1inhib_1 | 1.0044235 |
| IM_none_mTORC1inhib_2 | 1.1910875 |
| IM_none_Oligo_1 | 0.6253366 |
| IM_none_Oligo_2 | 1.0088429 |
| IM_none_MPCinhib_1 | 1.1677240 |
| IM_none_MPCinhib_2 | 0.9341128 |
| IM_none_LDHinhib_1 | 1.0838948 |
| IM_none_LDHinhib_2 | 1.0119412 |
| IM_none_IL6_1 | 1.1521243 |
| IM_none_IL6_2 | 1.0656570 |
Removal of - Oligomycin - EGF positive - Growth medium - IL6 - IM HC neg - IM ins neg
I think we can see a pretty evident batch effect per replicate!
I think we can see a pretty evident batch effect per replicate!
Same thing here, the batch effect can seen and disappears with the limma::removeBatchEffect function. Meaning I need to include replicates in the design formula.
| x |
|---|
| Intercept |
| condition_AKT_inhibitor_vs_IM |
| condition_AMPK_activator_vs_IM |
| condition_ERK_inhibitor_vs_IM |
| condition_Growth_Medium_vs_IM |
| condition_IL6_vs_IM |
| condition_IM_CT_neg_vs_IM |
| condition_IM_EGF_pos_vs_IM |
| condition_IM_Glucose_neg_vs_IM |
| condition_IM_Glutamine_pos_vs_IM |
| condition_IM_HC_neg_vs_IM |
| condition_IM_Ins_neg_vs_IM |
| condition_LDH_inhibitor_vs_IM |
| condition_MPC_inhibitor_vs_IM |
| condition_mTORC1_inhibitor_vs_IM |
| condition_Oligomycin_vs_IM |
| replicate |
Maybe - Oligomycin vs IM - EGF vs IM - EGF vs Oligomycin
| x |
|---|
| Intercept |
| condition_IM_vs_IM_EGF_pos |
| condition_AKT_inhibitor_vs_IM_EGF_pos |
| condition_AMPK_activator_vs_IM_EGF_pos |
| condition_ERK_inhibitor_vs_IM_EGF_pos |
| condition_Growth_Medium_vs_IM_EGF_pos |
| condition_IL6_vs_IM_EGF_pos |
| condition_IM_CT_neg_vs_IM_EGF_pos |
| condition_IM_Glucose_neg_vs_IM_EGF_pos |
| condition_IM_Glutamine_pos_vs_IM_EGF_pos |
| condition_IM_HC_neg_vs_IM_EGF_pos |
| condition_IM_Ins_neg_vs_IM_EGF_pos |
| condition_LDH_inhibitor_vs_IM_EGF_pos |
| condition_MPC_inhibitor_vs_IM_EGF_pos |
| condition_mTORC1_inhibitor_vs_IM_EGF_pos |
| condition_Oligomycin_vs_IM_EGF_pos |
| replicate |
## R version 4.3.1 (2023-06-16 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19045)
##
## Matrix products: default
##
##
## locale:
## [1] LC_COLLATE=English_United States.utf8
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
##
## time zone: America/Los_Angeles
## tzcode source: internal
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] clusterProfiler_4.8.3 msigdbr_7.5.1
## [3] xlsx_0.6.5 pheatmap_1.0.12
## [5] ggrepel_0.9.3 biomaRt_2.56.1
## [7] cowplot_1.1.1 DESeq2_1.40.2
## [9] SummarizedExperiment_1.30.2 Biobase_2.60.0
## [11] MatrixGenerics_1.12.3 matrixStats_1.0.0
## [13] GenomicRanges_1.52.0 GenomeInfoDb_1.36.3
## [15] IRanges_2.34.1 S4Vectors_0.38.2
## [17] BiocGenerics_0.46.0 lubridate_1.9.2
## [19] forcats_1.0.0 stringr_1.5.0
## [21] dplyr_1.1.3 purrr_1.0.2
## [23] readr_2.1.4 tidyr_1.3.0
## [25] tibble_3.2.1 ggplot2_3.4.3
## [27] tidyverse_2.0.0 RColorBrewer_1.1-3
##
## loaded via a namespace (and not attached):
## [1] rstudioapi_0.15.0 jsonlite_1.8.7 magrittr_2.0.3
## [4] farver_2.1.1 rmarkdown_2.25 ragg_1.2.5
## [7] fs_1.6.3 zlibbioc_1.46.0 vctrs_0.6.3
## [10] memoise_2.0.1 RCurl_1.98-1.12 ggtree_3.8.2
## [13] htmltools_0.5.6 S4Arrays_1.0.6 progress_1.2.2
## [16] curl_5.0.2 gridGraphics_0.5-1 sass_0.4.7
## [19] bslib_0.5.1 plyr_1.8.9 cachem_1.0.8
## [22] igraph_1.5.1 lifecycle_1.0.3 pkgconfig_2.0.3
## [25] gson_0.1.0 Matrix_1.5-4.1 R6_2.5.1
## [28] fastmap_1.1.1 GenomeInfoDbData_1.2.10 aplot_0.2.2
## [31] digest_0.6.33 enrichplot_1.20.3 ggnewscale_0.4.9
## [34] colorspace_2.1-0 patchwork_1.1.3 AnnotationDbi_1.62.2
## [37] textshaping_0.3.6 RSQLite_2.3.1 labeling_0.4.3
## [40] filelock_1.0.2 fansi_1.0.4 timechange_0.2.0
## [43] httr_1.4.7 polyclip_1.10-6 abind_1.4-5
## [46] compiler_4.3.1 bit64_4.0.5 withr_2.5.1
## [49] downloader_0.4 BiocParallel_1.34.2 viridis_0.6.4
## [52] DBI_1.1.3 ggforce_0.4.1 MASS_7.3-60
## [55] rappdirs_0.3.3 DelayedArray_0.26.7 HDO.db_0.99.1
## [58] tools_4.3.1 scatterpie_0.2.1 ape_5.7-1
## [61] glue_1.6.2 nlme_3.1-162 GOSemSim_2.26.1
## [64] shadowtext_0.1.2 grid_4.3.1 reshape2_1.4.4
## [67] snow_0.4-4 fgsea_1.26.0 generics_0.1.3
## [70] gtable_0.3.4 tzdb_0.4.0 data.table_1.14.8
## [73] hms_1.1.3 tidygraph_1.2.3 xml2_1.3.5
## [76] utf8_1.2.3 XVector_0.40.0 pillar_1.9.0
## [79] yulab.utils_0.1.0 babelgene_22.9 rJava_1.0-6
## [82] splines_4.3.1 tweenr_2.0.2 treeio_1.24.3
## [85] BiocFileCache_2.8.0 lattice_0.21-8 bit_4.0.5
## [88] tidyselect_1.2.0 GO.db_3.17.0 locfit_1.5-9.8
## [91] Biostrings_2.68.1 knitr_1.44 gridExtra_2.3
## [94] svglite_2.1.2 xfun_0.40 graphlayouts_1.0.1
## [97] stringi_1.7.12 lazyeval_0.2.2 ggfun_0.1.3
## [100] yaml_2.3.7 evaluate_0.21 codetools_0.2-19
## [103] xlsxjars_0.6.1 ggraph_2.1.0 qvalue_2.32.0
## [106] ggplotify_0.1.2 cli_3.6.1 systemfonts_1.0.4
## [109] munsell_0.5.0 jquerylib_0.1.4 Rcpp_1.0.11
## [112] dbplyr_2.3.3 png_0.1-8 XML_3.99-0.14
## [115] parallel_4.3.1 blob_1.2.4 prettyunits_1.2.0
## [118] DOSE_3.26.2 bitops_1.0-7 tidytree_0.4.5
## [121] viridisLite_0.4.2 scales_1.2.1 crayon_1.5.2
## [124] rlang_1.1.1 fastmatch_1.1-4 KEGGREST_1.40.0